This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. This project seeks to compare the efficacy of data-independent acquisition (DIA) with data-dependent acquisition (DDA) strategies. This study is conducted with Saccharomyces cerevisiae, for which copy numbers of many proteins are known. Thus the protein sampling depth of each method can be examined.